Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics

Nucleic Acids Research, Feb 2016

It is being increasingly realized that nucleosome organization on DNA crucially regulates DNA–protein interactions and the resulting gene expression. While the spatial character of the nucleosome positioning on DNA has been experimentally and theoretically studied extensively, the temporal character is poorly understood. Accounting for ATPase activity and DNA-sequence effects on nucleosome kinetics, we develop a theoretical method to estimate the time of continuous exposure of binding sites of non-histone proteins (e.g. transcription factors and TATA binding proteins) along any genome. Applying the method to Saccharomyces cerevisiae, we show that the exposure timescales are determined by cooperative dynamics of multiple nucleosomes, and their behavior is often different from expectations based on static nucleosome occupancy. Examining exposure times in the promoters of GAL1 and PHO5, we show that our theoretical predictions are consistent with known experiments. We apply our method genome-wide and discover huge gene-to-gene variability of mean exposure times of TATA boxes and patches adjacent to TSS (+1 nucleosome region); the resulting timescale distributions have non-exponential tails.

A PDF file should load here. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser.

Alternatively, you can download the file locally and open with any standalone PDF reader:

https://nar.oxfordjournals.org/content/44/4/1630.full.pdf

Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics

Nucleic Acids Research Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics Jyotsana J. Parmar 1 Dibyendu Das 0 Ranjith Padinhateeri 1 0 Department of Physics, Indian Institute of Technology Bombay , Mumbai 400076 , India 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai 400076 , India It is being increasingly realized that nucleosome organization on DNA crucially regulates DNA-protein interactions and the resulting gene expression. While the spatial character of the nucleosome positioning on DNA has been experimentally and theoretically studied extensively, the temporal character is poorly understood. Accounting for ATPase activity and DNA-sequence effects on nucleosome kinetics, we develop a theoretical method to estimate the time of continuous exposure of binding sites of nonhistone proteins (e.g. transcription factors and TATA binding proteins) along any genome. Applying the method to Saccharomyces cerevisiae, we show that the exposure timescales are determined by cooperative dynamics of multiple nucleosomes, and their behavior is often different from expectations based on static nucleosome occupancy. Examining exposure times in the promoters of GAL1 and PHO5, we show that our theoretical predictions are consistent with known experiments. We apply our method genomewide and discover huge gene-to-gene variability of mean exposure times of TATA boxes and patches adjacent to TSS (+1 nucleosome region); the resulting timescale distributions have non-exponential tails. - One of the crucial contributor to cellular function and fate is the ‘state’ of its chromatin, which is a dynamic structure formed of DNA and myriads of proteins (1–3). The key constituents of the chromatin are nucleosomes––DNA wrapped around histone octamer (4). It is thought that one major role of nucleosomes is to occlude certain DNA sequences from getting exposed and thereby prevent uncontrolled binding of non-histone proteins at various crucial locations (5). However, during important cellular processes (e.g. transcription, replication and DNA-repair), nucleosome disassembly paves the way for local DNA accessibility (6,7). Once these processes are completed, the DNA typically wraps back and reassembles into nucleosomes (8). This constant wrapping, unwrapping and relocation of nucleosomes are assisted by ATP-dependent chromatin remodelers (e.g. RSC, SWI/SNF, ACF) (9–12). Thus the interplay of nucleosome dynamics and binding of non-histone proteins regulate the ‘state’ of chromatin and its corresponding functionality. A major focus of many recent experiments has been to understand the nature of positioning of nucleosomes along DNA and the factors that control this positioning. This is achieved by measuring a physical quantity known as nucleosome occupancy (8,13–18). It is the probability of coverage of a base pair (bp) of DNA by a nucleosome, obtained from an ensemble of cells under same conditions, using MNase digestion, chemical cleavage, etc. (13–15,18,19). Such studies over years have shown that the in vivo positioning is influenced by a number of factors such as ATP-dependent molecular machines (11,13), DNA sequence (15,20–22) and ‘barriers’ that create nucleosome free region (NFR) near transcription start site (TSS) (13,23,24). Even though the occupancy gives us an idea about the spatial heterogeneity of occluded regions along DNA, the quantity results from superposition of several frozen snapshots. Hence, it cannot give us information about the temporal variability of the occluded regions and accessibility of DNA, which is crucial for many cellular processes like gene regulation. It is known that gene regulation, transcription, etc. are kinetically driven processes with many non-histone proteins (transcription factors (TFs), TATA-binding protein (TBP) and RNA polymerase (RNAp) complex) binding on to the DNA competing with the nucleosomes. One crucial factor that controls the binding of these proteins is the availability of continuously exposed (empty, having no proteins bound) patches of DNA. The kinetics of nucleosomes play an important role in regulating this continuous exposure (25–27). For example, disassembly of nucleosomes is known to be important for exposure of TATA sites in promoters (19,28,29), while dynamics of +1 nucleosome is likely to influence the accessibility near TSS (30). Sliding of nucleosomes (31,32) as well as partial unwrapping/wrapping (33) of DNA at nucleosome edges may also contribute toward creating exposed regions along DNA. All such kinetic activities, which are stochastic, can collectively influence transcription levels and noise in gene expression. In this context, it is important to stress the difference between the study of temporal versus static positioning (occupancy) of nucleosomes. As shown in Figure 1(A and B), nucleosome with two sets of kinetic rates: (i) k+ = k− = 0.1s−1 or (ii) k+ = (...truncated)


This is a preview of a remote PDF: https://nar.oxfordjournals.org/content/44/4/1630.full.pdf

Jyotsana J. Parmar, Dibyendu Das, Ranjith Padinhateeri. Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics, Nucleic Acids Research, 2016, pp. 1630-1641, 44/4, DOI: 10.1093/nar/gkv1153